SpatialDecon-package {SpatialDecon} | R Documentation

## SpatialDecon: A package for computating the notorious bar statistic.

### Description

The SpatialDecon package estimates mixed cell type abundance in the regions of spatially-resolved gene expression studies, using the method of Danaher & Kim (2020), "Advances in mixed cell deconvolution enable quantification of cell types in spatially-resolved gene expression data." It is also appropriate to apply to bulk gene expression data.

### functions

Functions to help set up deconvolution:

- derive_GeoMx_background Estimates the background levels from GeoMx experiments

- collapseCellTypes reformats deconvolution results to merge closely-related cell types

- download_profile_matrix Downloads a cell profile matrix.

- safeTME: a data object, a matrix of immune cell profiles for use in tumor-immune deconvolution.

Deconvolution functions:

- spatialdecon runs the core deconvolution function

- reverseDecon runs a transposed/reverse deconvolution problem, fitting the data as a function of cell abundance estimates. Used to measure genes' dependency on cell mixing and to calculate gene residuals from cell mixing.

Plotting functions:

- florets Plot cell abundance on a specified x-y space, with each point a cockscomb plot showing the cell abundances of that region/sample.

- TIL_barplot Plot abundances of tumor infiltrating lymphocytes (TILs) estimated from the safeTME cell profile matrix

### Examples

    data(mini_geomx_dataset)
    data(safeTME)
    data(safeTME.matches)
    # estimate background:
    mini_geomx_dataset$bg <- derive_GeoMx_background(
      norm = mini_geomx_dataset$normalized,
      probepool = rep(1, nrow(mini_geomx_dataset$normalized)),
      negnames = "NegProbe"
    )
    # run basic decon:
    res0 <- spatialdecon(
      norm = mini_geomx_dataset$normalized,
      bg = mini_geomx_dataset$bg,
      X = safeTME
    )
    # run decon with bells and whistles:
    res <- spatialdecon(
      norm = mini_geomx_dataset$normalized,
      bg = mini_geomx_dataset$bg,
      X = safeTME,
      cellmerges = safeTME.matches,
      cell_counts = mini_geomx_dataset$annot$nuclei,
      is_pure_tumor = mini_geomx_dataset$annot$AOI.name == "Tumor"
    )

[Package SpatialDecon version 1.4.3 Index]